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Releasing the GitHub Portfolio
Published:
Today, Friday, 25 April 2025, I officially release this GitHub Portfolio. I began using this account to store code related to research data analysis. My previous projects were sufficiently handled using Excel and R for data processing. However, since the end of 2023, I’ve been involved in genomic and animal behavior research, which requires managing more complex datasets and workflows.
portfolio
Something Exciting will be Revealed Here
I’m working on it. Just little more patience.
publications
Microsatellite selection candidate associated with reproduction trait in Indonesian Friesian Holstein using published studies
Published in AIP Conference Proceedings, 2018
This study identify 7 microsatellites namely ETH152, ETH225, BM2113, INRA032, BM1824, BM1818 and MM12 were associated with calving ease, non-return rate and twinning.
Recommended citation: Vanessa, R., Prastowo, S., Nugroho, T., Widyas, N., Susilowati, A., & Sutarno, S. (2018). Microsatellite selection candidate associated with reproduction trait in Indonesian Friesian Holstein using published studies. In AIP Conference Proceedings (Vol. 2014, No. 1). AIP Publishing.
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Conventional and Mixed Model Approach to Estimate Heterosis of the Growth Traits in Boer Goat’s Crossbred Offspring Populations
Published in Caraka Tani: Journal of Sustainable Agriculture, 2019
This article was to compare heterosis estimated with conventional and mixed model approaches on Boer goat crossbred.
Recommended citation: Widyas, N., Prastowo, S., Nugroho, T., & Ratriyanto, A. (2019). Conventional and Mixed Model Approach to Estimate Heterosis of the Growth Traits in Boer Goat’s Crossbred Offspring Populations. Caraka Tani: Journal of Sustainable Agriculture, 34(1), 55-60.
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Crossbreeding strategy evaluation between Boer and local Indonesian goat based on pre-weaning traits
Published in International Journal of Agricultural Technology, 2021
This study is evaluated the crossbreeding strategy between Boer goat and Jawarandu goats by observing the pre-weaning traits hehritability and genetic correlation.
Recommended citation: Widyas, N., Nugroho, T., Ratriyanto, A., & Prastowo, S. (2021). Crossbreeding strategy evaluation between Boer and local Indonesian goat based on pre-weaning traits. International Journal of Agricultural Technology, 17(6), 2461-2472
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Candidacy of genes associated with economic traits for Madura cattle in Sonok area
Published in IOP Conference Series: Earth and Environmental Science, 2022
This study identify 18 gene were observed on Madura cattle and five gene responsible to economic trait (IGF-1, GH, GHR, LEP, MSTN)
Recommended citation: Nugroho, T., Maharani, D., & Widi, T. S. M. (2022). Candidacy of genes associated with economic traits for Madura cattle in Sonok area. In IOP Conference Series: earth and environmental science (Vol. 1001, No. 1, p. 012018). IOP Publishing.
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Protein-to-protein interaction of genes responsible for the economic trait of Madura Cattle: an in silico analysis
Published in IOP Conference Series: Earth and Environmental Science, 2022
This study analyze interaction of Insulin-like growth factor-1 (IGF-1), Growth hormone (GH1), Growth hormone receptor (GHR), Myostatin (MSTN), and Leptin (LEP).
Recommended citation: Nugroho, T., & Prastowo, S. (2022). Protein-to-protein interaction of genes responsible for the economic trait of Madura Cattle: an in silico analysis. In IOP Conference Series: Earth and Environmental Science (Vol. 1114, No. 1, p. 012084). IOP Publishing.
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Factors affecting post-weaning growth of Boer and Boer cross goats in a closed breeding farm population
Published in Jurnal Sain Peternakan Indonesia, 2023
This paper analyze effect of genetic group, buck, litter size, birth season, weaning season-year, and their interactions to the post-weaning growth of Boer and Boer cross goats’
Recommended citation: Nugroho, T., Widyas, N., Widi, T. S. M., & Prastowo, S. (2023). Factors affecting post-weaning growth of Boer and Boer cross goats in a closed breeding farm population. Jurnal Sain Peternakan Indonesia, 18(4), 193-201.
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talks
Biological Processes and Pathways of the Heat Shock Protein Family and Their Relation to Cattle Behaviour in the Tropical Environment
Published:
Heat Shock Protein Family (HSPs) plays an important role in the heat stress of cattle. Heat stress, which is related to animal behavior, poses a challenge for the production system in tropical environments. This study aimed to identify the biological processes and pathways of the HSPs and their potential relationship to cattle stress behaviors in tropical environments. An in silico study was conducted using STRING v.11.5, a reliable database for protein-protein interactions. Eight HSPs in Bos taurus, including HSPB8, HSPB7, HSPE1, HSPD1, HSPA1A, HSPA6, HSP90AA1, and HSP90AB1, which were identified as responsible for heat tolerance in previous studies, were used for the analysis. A further literature review was conducted using the Scopus database to explore the potential relationship between the HSPs and cattle behavior. The results showed that all HSPs interacted with each other through 21 interaction edges. HSPA1A had the highest number of connections, while HSPB7 had the lowest. Eight biological processes and six KEGG pathways were found to be involved in the interactions between HSPs. Combination of 3-7 HSPs were found to interact within biological process, including response to stress, protein folding, cellular response to stress, cellular response to unfolded protein, response to temperature stimulus, protein refolding, chaperone cofactor-dependent protein refolding, and cellular response to heat. Combination of 2-3 HSPs were involved in KEGG pathways, namely legionellosis, antigen processing and presentation, estrogen signaling pathway, protein processing in endoplasmic reticulum, longevity regulating pathway - multiple species, and toxoplasmosis. Furthermore, based on the literature review, HSPD1, HSPA1A, HSP90AA1, and HSP90AB1 expression was found to be associated with cattle behavior and physiology under heat stress conditions. Based on bioinformatics analysis, we demonstrate that each HSPs interacts with each other to control heat stress mechanisms, is involved in physiological pathways, and has relationships with cattle behavior under heat stress in tropical environments.
The role of Dopamine Receptor Family on cattle behavior: an in silico study
Published:
The Dopamine Receptor (DR) family, which is divided into five subtypes (D1, D2, D3, D4, D5), is implicated in various neurological processes. This paper aimed to analyze the role of the DR family in cattle behavior through an in silico study. Several steps of analysis were carried out. Initially, the five subtypes of DR (DRD1, DRD2, DRD3, DRD4, and DRD5) were filtered from the ‘Behavior’ or GO:0007610 biological process annotation in the Gene Ontology database (https://geneontology.org/). Subsequently, the fifth DR on Bos taurus and Bos indicus × Bos taurus (hybrid cattle) were used as inputs for protein-to-protein interaction analysis using the STRING database (https://string-db.org/). Finally, a similarity check of DR nucleotides and proteins among Bos taurus, Bos indicus, and hybrid cattle was done using BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi). Results showed that the DR family was associated with 29 types of ‘Behavior’ biological processes in various species. In Bos taurus, the DR protein interactions were divided into two clusters, DRD5-DRD1-DRD2 and DRD3-DRD4. However, in hybrid cattle, all DRDs interacted with each other. Four DRs (DRD2, DRD3, DRD4, DRD5) were found to interact in the ‘Behavior’ biological process in both Bos taurus and hybrid cattle. The nucleotides and proteins of the DR family in the three types of cattle showed more than 99% similarity, except for the DRD3 in hybrid cattle. It is concluded that the DR family plays an important role in cattle behavior. Further association studies are needed to proof this result.
An in-silico study on the diversity and protein-to-protein interactions of the serotonin receptors family and its role in cattle behaviour
Published:
Serotonin, also known as 5-hydroxytryptamine (5-HT), plays a crucial role in a wide range of physiological functions. This paper aims to analyze the protein-to-protein interactions within the serotonin receptor family and its role in cattle behavior. Thirteen serotonin receptors (HTR1A, HTR1B, HTR1D, HTR1E, HTR1F, HTR2A, HTR2B, HTR2C, HTR3A, HTR4, HTR5A, HTR6, HTR7) were used in this study. First, we compared the profile of each serotonin receptor protein in Bos taurus, Bos indicus, and Bos taurus × indicus. Subsequently, these profiles were used as input in the STRING database for protein-to-protein interaction analysis. A biological process related to cattle behavior was selected. The results showed diverse serotonin receptor proteins among cattle species, with HTR3A playing a significant role in mediating their interactions. The interactions related to behavior included the serotonin receptor signaling pathway, G protein-coupled receptor signaling pathway coupled to cyclic nucleotide second messenger, regulation of biological quality, adenylate cyclase-inhibiting serotonin receptor signaling pathway, blood vessel diameter maintenance, vasoconstriction, and regulation of behavior. Four serotonin receptor (HTR1A, HTR1B, HTR1D, HTR2B) were involved in regulation of ‘behaviour’ biological processes. In conclusion, the serotonin receptor family was diverse among cattle species and played a crucial role in cattle behavior.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.